Reading input alignment file to find conserved blocks of secondary structure The input structure based alignment from Comparer _____________________________________________ >P1;d1glaf- ----------------------------------CCCCCCC-CEEEECCCCEEEECHHHCCC---HHHHCCCCCEEEEEEEC----------CCEEECCCC---------------EEEEEECC------CCCEEEEEECCCCEEEEECCCCHHHHCCCCEEECCCCCCEE-CCCEEEEECHHHHHHHC-CCCCCEEECCCCCCCEEEE-CCCEECCCCCEEEEEEC------------------------------- >P1;d1gpra- ----------------------------------CCCCCCCCCCCCCCCCCEEEEEHHHCCC---HHHHCCCCCEEEEEEEC----------CCEEECCCC---------------EEEEEECC------CCCEEEEEECCCCEEEEECCCCCHHHCCCCEEECCCCCCEECCCCEEEEECHHHHHHHCCCCCEEEEECCCCCCCEEEECCCCEECCCCCCCEEEE-------------------------------- >P1;d1qwya- CCCCCEEEECCCCCEEEECCCCCCHHHHHCCCCCEEEECCCCCEEEECC--CCCCCCCCCEECCCCCCCCCCCCCCCCCCCEEHHHHHHHCCCCCCCCCHHHCCCCCCCCCHHHHCCCEEECCEECCCCCEECCEEEECCCCCEEECCCC----------EEEEEEEEECCCCEEEEEEEEC-------CCCEEEEEEEEC----EECCCCCCEECCC-CEEEECCCCCCCCCCEEEEEEEECEECHHHEECCHHHHC PSA >P1;d1glaf- ----------------------------------d8a89a9-82202000226037056053---74026354120000607----------873000007---------------15085039------110002060959050101002707708350063508673a0-23620050417305840-31100000213b7087052-38880621632003064------------------------------- >P1;d1gpra- ----------------------------------7445296542210000115025064053---95015464520000407----------503000003---------------05036038------2400020300263301010007077182930514075544061054004072a5076605201000002507bb2604131998082646500416-------------------------------- >P1;d1qwya- 5416173442a84210004738167713686515020619874201009--2105a09241518160a343b40000003003294177590428402081179b8806919202748433326807ca750200001054524030005----------0302301000000000000305-------b36200000001----2031349580814-520020021010754000000034000053046059006 Translating the sequences ----------------------------------CCCCCCC-CEEEECCCCEEEECHHHCCC---HHHHCCCCCEEEEEEEC----------CCEEECCCC---------------EEEEEECC------CCCEEEEEECCCCEEEEECCCC*HHHCCCCEEECCCCCCEE-CCCEEEEECHHHHHHHC-CCC**EEECCCCCCCEEEE-CCCEECCCCCEEEEEEC------------------------------- ----------------------------------CCCCCCCCC****CCCCEEEE*HHHCCC---HHHHCCCCCEEEEEEEC----------CCEEECCCC---------------EEEEEECC------CCCEEEEEECCCCEEEEECCCC*HHHCCCCEEECCCCCCEECCCCEEEEECHHHHHHHCCCCCEEEEECCCCCCCEEEECCCCEECCCCC**EEEE-------------------------------- **************************************CCCCCEEEECC--****C***C*********CCCCC******************CC***CC*******************EEE*C*********C*EEEE*CCCCEEE**CC----------EEE********CC**EEEEE**-------CCC*EEEEE**C----EE**CCCCEECCC-CEEEE**C******************************* 51261.tem _________________________________ ----------------------------------CCCCCCCCCEEEECCCCEEEECHHHCCC---HHHHCCCCCEEEEEEEC----------CCEEECCCC---------------EEEEEECC------CCCEEEEEECCCCEEEEECCCC*HHHCCCCEEECCCCCCEECCCCEEEEECHHHHHHHCCCCCEEEEECCCCCCCEEEECCCCEECCCCCEEEEEEC------------------------------- Structural block scores 0 33 - 4.0 M 75.0 75.0 4.1 34 42 C 4.4 M 16.8 5.1 4.1 43 46 E 4.0 M 1.5 1.2 0.8 47 50 C 4.5 M 0.5 0.2 39.8 51 54 E 4.0 M 2.8 2.0 2.0 56 58 H 4.0 M 3.7 3.3 3.7 59 61 C 4.3 M 2.7 2.7 3.3 62 64 - 4.0 M 75.0 75.0 3.3 65 68 H 4.0 M 3.2 3.8 4.9 69 73 C 5.0 H 3.8 4.8 4.5 74 80 E 4.0 M 1.1 0.9 0.4 82 91 - 4.0 M 75.0 75.0 4.7 92 93 C 5.0 H 7.5 2.5 3.0 94 96 E 4.0 M 1.0 1.0 4.0 97 100 C 4.5 M 1.8 0.8 2.8 101 115 - 4.0 M 75.0 75.0 5.4 116 121 E 4.5 M 3.2 2.3 4.2 122 123 C 4.5 M 6.0 5.5 4.0 124 129 - 4.0 M 75.0 75.0 7.5 130 132 C 4.3 M 0.7 2.0 2.3 133 138 E 4.7 H 1.3 0.8 0.2 139 142 C 5.0 H 5.8 2.8 4.0 143 147 E 4.6 H 1.4 1.0 1.4 148 151 C 4.5 M 2.2 1.8 38.8 153 155 H 4.0 M 4.7 5.0 75.0 156 159 C 4.0 M 4.0 5.5 75.0 160 162 E 5.0 H 3.0 2.0 1.0 163 168 C 4.0 M 4.8 4.2 1.0 169 170 E 4.0 M 5.2 2.0 0.0 171 174 C 4.2 M 21.5 3.0 0.0 175 179 E 5.0 H 1.4 1.6 0.6 181 187 H 4.0 M 4.0 5.2 65.0 188 192 C 4.4 M 16.0 1.6 19.5 193 197 E 4.6 H 0.0 0.0 0.0 198 204 C 4.1 M 4.6 5.6 43.0 205 208 E 4.5 M 3.5 2.8 1.5 209 212 C 4.8 H 23.5 5.5 5.2 213 214 E 5.0 H 4.0 4.0 4.0 215 219 C 4.8 H 3.6 5.2 18.6 220 225 E 4.3 M 1.8 2.7 0.7 227 257 - 4.0 M 75.0 75.0 2.0 >>>>>>